MolNFT v1 · #52345 · protein
X-ray structure of dpsa from thermosynechococcus elongatus
2VXX · Starvation induced DNA binding protein: “X-ray structure of dpsa from thermosynechococcus elongatus”. X-ray diffraction, 2 ligands (ZN, FE), 7 pockets (best druggability 0.52). MolNFT v1 #52345 on GenesisL1: 3D structure, binding…
- PDB
- 2VXX
- Type
- protein
- Length
- 690 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Starvation induced DNA binding protein
- UniProt
- Q8DL82
- Ligands
- ZN, FE
- Pockets
- 7 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 70% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Starvation induced DNA binding protein | protein | 172 | 70% helix, 1% strand | Q8DL82 |
| B, C | Starvation induced DNA binding protein | protein | 173 | 69% helix, 1% strand | Q8DL82 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D
- FE · Fe (III) ion · metal · 2 copies · chains D, A, C
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains B, C, D
- PG4 · Tetraethylene glycol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.52 | 0.76 | 27 | empty |
| 2 | 182 | 0.46 | 0.75 | 31 | empty |
| 3 | 109 | 0.46 | 0.79 | 25 | empty |
| 4 | 55 | 0.35 | 0.78 | 14 | empty |
| 5 | 78 | 0.34 | 0.75 | 14 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1943 Ų buried · 34 hydrogen bonds · protein-protein
- A–B · 1926 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 876 Ų buried · 14 hydrogen bonds · protein-protein
- A–D · 826 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2VXX · X-ray structure of DpsA from Thermosynechococcus elongatus · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8DL82
- Elsewhere: RCSB PDB 2VXX · PDBe 2VXX · UniProt Q8DL82
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